Bacteria Sample Count Project

This project processes a dataset of bacteria samples and generates reports in CSV, JSON, and XML formats.

Directory Structure

• .gitattributes: Git attributes configuration.
• count_samples.py: Python script to process the data and generate reports.
• README.md: This file.
• report.csv: Generated report in CSV format.
• report.json: Generated report in JSON format.
• report.xml: Generated report in XML format.

File Descriptions

count_samples.py

This script traverses the directory structure containing the bacteria sample data, counts the samples, and generates reports in three different formats: CSV, JSON, and XML.

report.csv

This file contains the sample report in CSV format. Each line represents a sample in the format Genus,Species,Count.

report.json

This file contains the sample report in JSON format. The structure is a dictionary where the keys are the genera and the values are dictionaries with the species and their respective counts.

report.xml

This file contains the sample report in XML format. The structure is an XML tree where each genus is a node containing child nodes for each species with their respective counts.

Running the Script

To run the script and generate the reports, simply execute the following command in your terminal:

python count_samples.py

Example Usage

Below is an example of a portion of the report.json file:

{
    "Streptococcus": {
        "Agalactiae": 8,
        "Dysgalactiae": 12,
        "Mitis": 4,
        "Parasanguinis": 12,
        "Pneumoniae": 24,
        "Pyogenes": 30,
        "Salivarius": 35,
        "Sanguinis": 8
    },
    "Sutcliffiella": {
        "Cohnii": 36
    },
    "Vibrio": {
        "Alginolyticus": 12,
        "Cholerae": 218,
        "Diazotrophicus": 4,
        "Harveyi": 11
    }
}